void IDFilter::filterIdentificationsByProteins(const ProteinIdentification& identification,
const vector<FASTAFile::FASTAEntry>& proteins,
ProteinIdentification& filtered_identification)
{
String protein_sequences;
String accession_sequences;
vector<ProteinHit> filtered_protein_hits;
ProteinHit temp_protein_hit;
filtered_identification = identification;
filtered_identification.setHits(vector<ProteinHit>());
for (Size i = 0; i < proteins.size(); i++)
{
accession_sequences.append("*" + proteins[i].identifier);
}
accession_sequences.append("*");
for (Size i = 0; i < identification.getHits().size(); i++)
{
if (accession_sequences.find("*" + identification.getHits()[i].getAccession()) != String::npos)
{
filtered_protein_hits.push_back(identification.getHits()[i]);
}
}
filtered_identification.setHits(filtered_protein_hits);
filtered_identification.assignRanks();
}
void IDFilter::removeUnreferencedProteinHits(const ProteinIdentification& identification, const vector<PeptideIdentification> peptide_identifications, ProteinIdentification& filtered_identification)
{
const String& run_identifier = identification.getIdentifier();
// build set of protein accessions that are referenced by peptides
set<String> proteinaccessions_with_peptides;
for (Size i = 0; i != peptide_identifications.size(); ++i)
{
// run id of protein and peptide identification must match
if (run_identifier == peptide_identifications[i].getIdentifier())
{
const vector<PeptideHit>& tmp_pep_hits = peptide_identifications[i].getHits();
// extract protein accessions of each peptide hit
for (Size j = 0; j != tmp_pep_hits.size(); ++j)
{
const std::vector<String>& protein_accessions = tmp_pep_hits[j].getProteinAccessions();
for (Size k = 0; k != protein_accessions.size(); ++k)
{
String key = protein_accessions[k];
proteinaccessions_with_peptides.insert(key);
}
}
}
}
// add all protein hits referenced by a peptide
const vector<ProteinHit>& temp_protein_hits = identification.getHits();
vector<ProteinHit> filtered_protein_hits;
for (Size j = 0; j != temp_protein_hits.size(); ++j)
{
const String& protein_accession = temp_protein_hits[j].getAccession();
if (proteinaccessions_with_peptides.find(protein_accession) != proteinaccessions_with_peptides.end())
{
filtered_protein_hits.push_back(temp_protein_hits[j]);
}
}
// copy identification
filtered_identification = identification;
// assign filtered hits to protein identification
filtered_identification.setHits(filtered_protein_hits);
}